Re: Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation)

From: David Case <>
Date: Thu 28 Mar 2002 10:40:16 -0800

On Thu, Mar 28, 2002, Wu, JianHui(IAF)(LAVAL) wrote:

> (1)
> While trying to run MD with GB (igb=1 gbsa=1)on a protein of 250 residues,
> Sander stop with error message 'Memory not enough, increase MATOM in
> nmr.h'. The message is clear enough but it seems nmr.h is related to nmr
> refinement and I never try to use nmr restraint here. Do I have other choice
> other than increase MATOM ...

No other choice. The GB module uses data structures set up in NMR.h.

> (2)
> Some single-point mutation would bring large conformational change. I can
> not afford explicit water simulation and GB or GB/SA in amber 6.0 become my
> choice. Perhaps a couple ns MD simulation with GB or GB/SA is good enough to
> address the issue? I am sure a lot of other amber users try this before. Do
> you have any luck? My protein has 250 residues. Any suggestion is greatly
> appreciated.

Seeing the appropriate large conformational changes upon point mutations
is a questionable goal, no matter how much computer time you have. You
should certainly be aware that GB force fields are much less mature than
the more traditional explicit water ones. Using GB is still a experimental
option at this point, so please proceed with that in mind.

..good luck..dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Thu Mar 28 2002 - 10:40:16 PST
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